Recently developed high density tissue microarray technology involves arraying up to thousands of cylindrical tissue cores from individual tumors on a tissue microarray (see, e.g. Kononen et al. Nat Med. 1998 July; 4(7):844-7). More than two hundred serial sections can then be made from an individual microarray block and used for analysis of DNA, RNA, and/or proteins on a single glass slide. The technology is useful in that it allows rapid analysis of a large number of samples so that the statistical relevance of new markers can be determined in a single experiment. In addition, altered expression levels can be correlated to amplification or deletion events in specific tumor samples using serial sections, allowing simultaneous determination of gene copy number and expression analysis of candidate pathogenic genes and suppressor genes. Arrays have been made containing numerous tumor types (see, e.g. Schraml et al. Clin Cancer Res. 1999 August; 5(8):1966-75) as well as multiple stages and grades within individual tumor types (see, e.g. Moch et al. Am J Pathol. 1999 April; 154(4):981-6; Bubendorf et al. Cancer Res. 1999 Feb. 15; 15;59(4):803-6 and Bubendorf et al. J Natl Cancer Inst. 1999 Oct. 20; 91(20):1758-64). This new technology has already proven useful for rapidly characterizing the prevalence and prognostic significance of differentially expressed genes identified using cDNA array technology (see, e.g. Bubendorf et al. J Natl Cancer Inst. 1999 Oct. 20; 91(20):1758-64; Moch et al. Verh Dtsch Ges Pathol. 1999; 83:225-32. German and Barlund et al. J Natl Cancer Inst 2000 Aug. 2; 92(15):1252-9) as well as genes involved in cancer development and progression (see, e.g. Bubendorf et al. Cancer Res. 1999 Feb. 15; 59(4):803-6 and Bubendorf et al. J Natl Cancer Inst 1999 Oct. 20; 91(20):1758-64). Tissue microarrays have also been useful in identifying genes that are targets of chromosomal amplification (see, e.g. Barlund et al. Cancer Res. 2000 Oct. 1; 60(19):5340-4 and Richter et al. Am J Pathol. 2000 September; 157(3):787-94) as well as to study the expression patterns of putative tumor suppressor genes (see, e.g. Bowen et al. Cancer Res. 2000 Nov. 1; 60(21):6111-5).
A variety of technical problems exist with the current methodology, however, relating to the fact that the arrayed samples have to be pre-fixed and embedded in paraffin. The quality of the studies performed on sections from tissue array technology may be limited by the fixation methods used on the original sample. Buffered formalin solutions (and related compounds) are among the most widely used tissue fixatives. These chemicals fix the tissue by acting as progressive cross linkers between proteins and nucleic acids, by introducing modifications in RNA (adding mono-methyl groups to its bases), and by producing coordinate bonds for calcium ions; these processes can damage RNA and alter target antigenic structure by blocking or damaging antibody binding sites (see, e.g. Masuda et al. Nucleic Acids Res. 1999 Nov. 15; 27(22):4436-43 and Werner et al. Am J Surg Pathol. 2000 July; 24(7):1016-9. Review). Formalin fixation-induced alterations can make in-situ analysis of DNA, RNA, and proteins suboptimal and variations in the duration of fixation can effect the quality and reproducibility of results (see, e.g. Kononen et al. Nat Med. 1998 July; 4(7):844-7; Werner et al. Am J Surg Pathol. 2000 July; 24(7):1016-9, Review and Specht et al. Am J Pathol. 2001 February; 158(2):419-429). Artisans attempt to overcome fixation problems for FISH by uniformly pre-fixing tissues in cold ethanol and embedding in paraffin (see, e.g. Kononen et al. Nat Med. 1998 July; 4(7):844-7), but this approach is not optimal for array analysis of some proteins or for RNA using in situ hybridization. Paraffin embedding of ethanol-fixed tissue does not prevent RNA degradation (see, e.g. Goldsworthy et al. Mol Carcinog. 1999 June; 25(2):86-91). In addition, while ethanol fixation of tissue and subsequent paraffin embedding circumvents formalin fixation-related problems introduced by crosslinking, there are still problems relating to the embedding, and/or deparaffinization processes such as temperature-induced antigenic alterations introduced during the embedding process (see, e.g. Werner et al. Am J Surg Pathol. 2000 July; 24(7):1016-9, Review; Battifora et al. J Histochem Cytochem. 1986 August; 34(8):1095-100 and Penault-Llorca et al. J Pathol. 1994 May; 173(1):65-75). 
Consequently there is a need in the art to identify additional methods that allow for the optimal preservation of biological molecules such as polypeptides and polynucleotides to be analyzed in such arrays. The present invention meets this need in the art by providing methods that circumvent problems associated with traditional paraffin arrays.